Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches.

ABSTRACT: The problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were shown to store the strongest mutual information (MI) signal to discriminate MSA concatenations with the largest fraction of correct pairings. Although that signal might be of practical relevance in the search for an effective heuristic to solve the problem, the number of MSA concatenations with near-native MI is large, imposing severe limitations. Here, a Genetic Algorithm that explores possible MSA concatenations according to a MI maximization criteria is shown to find degenerate solutions with two error sources, arising from mismatches among

SUBMITTER: Pontes C 

PROVIDER: S-EPMC7994710 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature